I finally had some time to digest Diana's article and wanted to comment on a couple things.
Once I realized that indeed is probably FTB, the background level concept was what my intuition was telling me made the most sense. Due to how hard it is to completely eradicate these bacteria, how frequent they are in aquariums, and for the following reasons.
In my case, I acquired a 55g with two fish from a friend. It was fully established (5 yrs or so) and after giving the fish away (cichlids) I started a community tank. Since the tank was cycled I stocked it fairly quickly, within 3-4 months I had most of the fish I wanted in there.
Except some neons that died after a month in the tank, none of the other fish seemed ill. Water parameters never got out of whack, and I only had one Ich out brake for the next 5 months. Then, one day one of my stigmata loaches developed a curved spine and started to lose weight, another (out of 4) started swimming erratically. Took both fish out, euthanized one and the other died in a hospital tank. That is when I started doing research, and concluded that it was either parasites or Fish TB. So I treated for parasites.
For 2-3 months after that, everything was fine so I acquired 4 GBR's. Again, for another 4-5 months everything went well until one day, with NO symptoms (that I could tell), one of my paired/breeding angel fish died, I didn't understand, maybe I was just overstocked (~20+ growing fish).
Then I moved out of State. All the fish made the 900mi. drive, but after 2-3 weeks the GBR's started dropping like flies and my betta developed the bloated stomach with wasted body sintoms. The GBR's all got progressively worse hollow bellys and after a couple weeks they all passed, while the betta was just hanging in there. I thought for sure parasites, and maybe the new water weakened the fish, while TB was in the back of my mind. So I treated for parasites with quick cure, and after a month I acquired 4 new fish, they all died within 2 weeks, but some had stringy feces, so I kept thinking maybe it is hard core parasites...
At this point I decided that I am not going to get any new fish, upgrade to a 120g to give a better environment to the rest of my stock (~20 fish now), nuked the 55g, and made it bare bottom with decorations to keep as hospital tank until the 120g cycled. I treated with Flub. for parasites and waited, soon enough, I got a nitrite spike on the 55g and lost 2 more fish despite my efforts with WCs, and the betta was so wasted I euthanized him.
So after a couple more weeks of daily WC and a lot of observation everything was well. I started introducing the fish from the 55g, that looked healthy and never displayed any symptoms whatsoever, into the 120g. At this point, only the fish that had been completely healthy for the 12+ months that I've had them were transferred to the 120g.
Then I found your thread and the TB diagnose, kicked myself in the head, since I have now introduced "healthy" carriers of the disease to my new tank (potentially) and I am pretty sure it is TB. That is why Option 2 is what I am doing now. I will keep transferring the fish in the 55g little by little to the 120g.
Conclusion: Basically, I've had a contaminated aquarium for probably almost 1 year now, and most of my fish, about 80%, seem just carriers/survivors. I believe that except in two occasions were deaths happened for "no reason", the flares were always months apart and due to some concrete environmental change in combination with overstocking; and also when new fish with no immunity were introduced.
So, since I am moving again in 6 months, I am going to commit to not getting any new fish, buying a UV sterilizer and see what happens. If the fish keep getting sick I will euthanize right away.
After I get established at a new place, and if my fish survive for another few months, I will seriously consider the "Sentinel" idea for my QT tank and a 2-3 month QT for any new additions. If I lose all my stock, I will sanitize the tank as much as I can (probably with a combo of different sanitizing agents) and turn the 120g into a salt water tank, and do something different with the hobby in order to keep my sanity.
(Sorry for the long post, English is my second language and I was trying to explain everything without confusing people)
[...] My initial plan was to go for Option 2, but as all this has sunk in over the last few days I've begun to wonder if some variety of nuke is somewhat inevitable simply on the basis of having to protect my own health. [...] On top of it all, I'd feel bad introducing any new fish to the tank, which wasn't even fully stocked yet, because it'd potentially be a death sentence!
That's not to say that I've ruled out Option 2 yet, [...]
The reason I'm looking at a one year QT for those guys is because those specific species are known to be especially vulnerable and because I positively know they've been exposed to it.
When it comes to QTing new arrivals, I'm also dealing with the same questions you're asking. I don't think a year would be necessary. A couple months ago I started practicing a 1 month QT, prior to that (when I got these guys) I was only using a week. Now I'm considering 1.5-2 months and might go as high as 3. It's certainly possible for TB to elude you longer than that, but there has to be a point of "acceptable risk" and I'm guessing most fish will begin to show symptoms within that time frame if they have it. Not an expert opinion, of course, but that's the direction I'm leaning.
Please let us know what you decide to do, both for your tanks and QT procedures!
Side note for FreshtoSalt: read her QT recommendations, it seems like 2-3 months is a good target.